[gmx-users] convergence of bilayer simulation

[Justin Lemkul]

On 7/11/19 12:14 PM, Prasanth G, Research Scholar wrote:
> Dear Roshan,
> Thank you for your response. I thought that the lipid also behaves as a
> solvent in the case of membrane simulation. we even try to make sure the
> set temperature (starting from equilibration) is beyond the phase
> transition temperature. I wonder what sort of impact this will have on rmsd
> and how effective it can be, to know weather the bilayer is equilibrated or
> not.
> I will surely give it a try.
> For now, I have calculated the APL (Area per lipid) and found that it was
> around 62 Angstrom (square). I am working on POPC, and this value is close
> to the reported APL of 65 Angstrom (square).
> I have also checked the dimensions of the box along the simulation and
> found it to not fluctuate much.
> I am hoping this would be sufficient.

RMSD will tell you nothing in a membrane. Area per lipid, bilayer 
thickness, lipid diffusion, etc. are what you should look at.

-Justin

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Justin A. Lemkul, Ph.D.
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